Combinatorial chemistry is one of the important new methodologies developed in the pharmaceutical, agrochemical, and biotechnology industries to reduce the time and costs associated with producing effective and competitive new drugs. Simply put, combinatorial chemistry is used to create large populations of molecules, or libraries that can be screened efficiently in large numbers for molecules having a specific bioactivity, as indicated initially by detection of binding between one or more compounds in the library with a target molecule, commonly a drug target. By producing larger, more diverse compound libraries, the probability of finding novel compounds of significant therapeutic and commercial value is increased. As with traditional drug design, combinatorial chemistry relies on organic synthesis methodologies. The difference is the scope, instead of synthesizing a single compound; combinatorial chemistry exploits automation and miniaturization to synthesize large libraries of compounds. Libraries of biopolymers may be prepared by the sequential synthesis based on randomized addition of amino acid, nucleotide, or sugar residues, or combinations thereof, to form peptides, RNAs, polysaccharides, glycosaminoglycans or the like, thereby to prepare a random mixture of oligomers. Techniques suitable for preparing protein or peptide libraries at the nucleic acid level by phage display and similar technologies also are known.
In brief, a common feature of the screening methods used in drug discovery is that they comprise a first screening, wherein widely diverse drug candidates are screened, which is followed by a subsequent screening wherein a second diversity of candidates, created based on the result of the first step, is screened.
U.S. Pat. No. 6,794,148 (Perceptive) relates to methods for screening a sample to select a ligand to a target of interest and for obtaining information about the ligand and its binding characteristics. More specifically, the disclosed methods involve combining a solution of heterogeneous ligands with the target of interest to screen the ligands on the basis of one or more binding characteristics. Ligands having the first binding characteristic bind to the target of interest thereby to form a target/ligand complex. The complex may then optionally be separated from unbound components. The complex or unbound component then is introduced to a second “dimension” capable of separating components based on a second binding characteristic. The sample solution may be obtained by the digestion of any protein, and the target may be immobilized such as on a column. Thus, in this method, the ligand diversity is provided in the solution, while the target of interest will be immobilised to a solid support. The disclosed method is useful in the preparation of pharmaceutically active compositions.
U.S. Pat. No. 6,372,425 (Merck Co. Inc.) relates to large scale affinity chromatography of macromolecules, and more specifically to a method of purifying antibodies which bind to a ligand, wherein the antibodies are present in an impure solution comprising:    (1) selecting a ligand comprising the steps of:    (a) preparing a phage expression library expressing a plurality of oligonucleotides comprising selected principle neutralization epitope (SPNE) candidate oligonucleotides;    (b) screening the phage library to determine which candidate oligonucleotide is a SPNE of the macromolecule by a process comprising attaching an essentially pure preparation of antibody to a solid-phase support and incubating the solid-phase supported antibody with the phage library to effect binding of SPNE to the solid-phase supported antibody;    (c) determining association constants and dissociation constants of SPNE-antibody interactions using surface plasmon resonance and selecting a ligand from the SPNEs identified,    (2) replicating the ligand to produce ligands;    (3) binding the ligands to a support matrix to produce bound ligands;    (4) performing column chromatography on the impure solution containing the antibodies using a chromatography column comprising the bound ligands.
Thus, liquid chromatography has been frequently used as a tool in the screening of combinatorial libraries, especially in the drug industry. However, once one specific biotechnologically produced drug candidate, such as a protein drug candidate, has been selected from the screening, there is still the substantial effort of preparing a reliable method for its manufacture. Such manufacture commonly includes the steps of genetical manipulation of a cell, such as E.coli; fermentation of such cells to express the protein drug; and finally an efficient purification scheme to result in a pharmaceutically acceptable purity in sufficient yields. Again, liquid chromatography is often used as one step or as a series of purification steps.
There are many well known principles of chromatography, such as affinity chromatography, wherein the biological affinity between two species is utilized, such as an antigen as the ligand which binds antibody targets, an enzyme ligand which binds target receptors etc; ion exchange chromatography, which utilize the charge attraction between a ligand and an oppositely charged target; and hydrophobic interaction chromatography, wherein hydrophobicity of ligands is utilized to interact with hydrophobic targets. A more recent chromatography principle which uses a mixture or combination of interactions is known as multimodal chromatography. For example, Johansson et al (Journal of Chromatography A, 1016 (2003) 35-49: Preparation and characterization of prototypes for multi-modal separation aimed for capture of positively charged biomolecules at high-salt conditions) disclose that aromatic multi-modal cation exchanger ligands based on carboxylic acids seem to be optimal for the capture of proteins at high salt concentrations, which is often the case when a protein is purified from a fermentation feed. A common feature of the multi-modal cation exchange ligands disclosed is that they contain hydrogen acceptor groups close to carboxylic groups. Further, Johansson et al (Journal of Chromatography A, 1016 (2003) 21-33: Preparation and characterization of prototypes for multi-modal separation aimed for capture of negatively charged biomolecules at high-salt conditions) disclose that multi-modal anion exchanger ligands based on primary and secondary amines, or both, can be equally useful for the capture of proteins at high salt concentrations. These multi-modal anion exchangers comprise hydroxyl groups in the proximity of the ionic group.
U.S. Pat. No. 7,144,743 (Ciphergen Biosystems) relates to solid substrates and to processes of making and using them in the context of separation science and analytical biochemistry. More specifically, the solid substrate is comprised of a solid support; a monocyclic or polycyclic group that is heterocyclic, heteroaromatic, or aromatic and that is substituted with a sulfate, sulfonate, phosphate, or phosphonate group; and a linking group that comprises a mercapto-, ether-, or amino-containing moiety. The linking group links the monocyclic or polycyclic group to the solid support. One advantage of the present solid substrate described herein is its high selectivity and specificity for biological substances such as immunoglobulins, together with the avoidance of costly and often detrimental cleaning processes required for prior art substrates. Two different formats are contemplated in particular. In one format, the solid support is of the form typically used for chromatography media, that is, a bead or particle. These beads or particles are derivatized with the mixed mode ligand. The beads or particles form a chromatography medium that one can use to pack the column. In another format, the solid support takes the form of a chip, that is, a solid support having a generally planar surface to which the mixed mode ligand can be attached, covalently or otherwise. In such a biochip, or microarray, format, the substrate presents a generally planar surface to which is attached a capture reagent: in the present context, a combination of a linking group and a monocyclic or polycyclic group. Thus, a biochip presents a defined region or site, more typically, a collection of defined regions or sites, on which analytes may be captured selectively. Upon capture, analytes can be detected and, optionally, characterized by a variety of techniques.
Webb et al have described combinatorial ligand libraries, see poster from abc Technologies Conference, Basle, Switzerland, 26-27 Jan. 2005: ChemSpeed Generation of Combinatorial Libraries of Chromatography Media: Application to Purification of Therapeutic Proteins (Matthew J. Webb, Jim C. Pearson, Helen R. Tatton, Ben M. Beacom & Jason R. Betley). The ligands of this library were triazine ligands, which ligands are regarded as affinity ligands i.e. ligands which are capable of binding to one biological function class of proteins only. In fact, the Webb ligands are highly specific affinity ligands, as they are capable of interacting with one subclass of proteins only.
Several more recent patents and patent applications relate to various multi-modal ion exchange ligands for use in protein purification and other separation protocols. However, there exist numerous potentially useful multi-modal ion exchange ligand structures in theory, and there is up to date no efficient and systematic way of determining which is the optimal specific structure of a multi-modal ion exchange ligand for a given target.